# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 23:13:17 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: ~{N}-[[4-(pyrrolidin-1-ylmethyl)phenyl]methyl]-4-thiophen-2-ylcarbonyl-piperazine-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NCc1ccc(CN2CCCC2)cc1)N3CCN(CC3)C(=O)c4sccc4
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 M7T  M7T  ~{N}-[[4-(pyrrolidin-1-ylmethyl)phenyl]methyl]-4-thiophen-2-ylcarbonyl-piperazine-1-carboxamide  ligand  57  29  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_M7T
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 M7T  O1   O  O     0  -0.471   6.0174   0.3984  -1.1418
 M7T  C15  C  C     0   0.535   5.1687  -0.1414  -0.4471
 M7T  C16  C  CR5   0  -0.331   5.1510  -1.6234  -0.3542
 M7T  S    S  S2    0   0.245   5.0904  -2.4736   1.1443
 M7T  C19  C  CR15  0  -0.452   5.2872  -3.9814   0.3639
 M7T  C18  C  CR15  0  -0.184   5.3968  -3.8407  -0.9870
 M7T  C17  C  CR15  0  -0.182   5.3356  -2.4848  -1.3973
 M7T  N3   N  NT    0  -0.463   4.2701   0.5477   0.2935
 M7T  C14  C  CH2   0  -0.324   4.3500   1.9957   0.3770
 M7T  C13  C  CH2   0  -0.291   3.2484   2.6643  -0.4277
 M7T  C21  C  CH2   0  -0.319   2.9717   0.0450   0.7089
 M7T  C20  C  CH2   0  -0.301   1.8620   0.7124  -0.0919
 M7T  N2   N  NT    0  -0.514   1.9542   2.1584  -0.0062
 M7T  C    C  C     0   0.753   0.8716   2.9994  -0.0752
 M7T  O    O  O     0  -0.541   0.9821   4.1717  -0.4174
 M7T  N    N  NH1   0  -0.682  -0.3330   2.4662   0.2621
 M7T  C1   C  CH2   0  -0.314  -1.5223   3.2901   0.3194
 M7T  C2   C  CR6   0   0.054  -2.7530   2.4243   0.2941
 M7T  C12  C  CR16  0  -0.270  -3.0146   1.5979  -0.7993
 M7T  C11  C  CR16  0  -0.270  -4.1449   0.8004  -0.8313
 M7T  C5   C  CR6   0   0.081  -5.0488   0.7995   0.2320
 M7T  C4   C  CR16  0  -0.302  -4.7834   1.6154   1.3232
 M7T  C3   C  CR16  0  -0.293  -3.6495   2.4205   1.3538
 M7T  C6   C  CH2   0  -0.322  -6.2984  -0.0404   0.1808
 M7T  N1   N  NT    0  -0.423  -6.0615  -1.3581  -0.3536
 M7T  C10  C  CH2   0  -0.274  -7.2787  -2.1174  -0.5831
 M7T  C9   C  CH2   0  -0.468  -6.7793  -3.5400  -0.8427
 M7T  C8   C  CH2   0  -0.462  -5.4086  -3.5970  -0.1334
 M7T  C7   C  CH2   0  -0.272  -5.2501  -2.2123   0.4951
 M7T  H1   H  HCR5  0   0.305   5.3189  -4.8914   0.9433
 M7T  H2   H  HCR5  0   0.274   5.5254  -4.6718  -1.6647
 M7T  H3   H  HCR5  0   0.274   5.4170  -2.1601  -2.4249
 M7T  H4   H  HCH2  0   0.257   4.2514   2.2783   1.4291
 M7T  H5   H  HCH2  0   0.273   5.3213   2.3350   0.0285
 M7T  H6   H  HCH2  0   0.268   3.2954   3.7377  -0.2644
 M7T  H7   H  HCH2  0   0.234   3.4062   2.4827  -1.4983
 M7T  H8   H  HCH2  0   0.278   2.9005  -1.0275   0.5536
 M7T  H9   H  HCH2  0   0.258   2.8322   0.2410   1.7749
 M7T  H10  H  HCH2  0   0.244   1.9330   0.3921  -1.1391
 M7T  H11  H  HCH2  0   0.266   0.9156   0.3399   0.2904
 M7T  H12  H  HNH1  0   0.398  -0.3606   1.6286   0.8196
 M7T  H13  H  HCH2  0   0.242  -1.5350   3.9245   1.2117
 M7T  H14  H  HCH2  0   0.257  -1.5235   3.9575  -0.5430
 M7T  H15  H  HCR6  0   0.247  -2.3239   1.5793  -1.6344
 M7T  H16  H  HCR6  0   0.244  -4.3311   0.1586  -1.6836
 M7T  H17  H  HCR6  0   0.247  -5.4641   1.6226   2.1665
 M7T  H18  H  HCR6  0   0.249  -3.4616   3.0464   2.2185
 M7T  H19  H  HCH2  0   0.207  -6.7501  -0.0819   1.1878
 M7T  H20  H  HCH2  0   0.251  -7.0332   0.4581  -0.4605
 M7T  H22  H  HCH2  0   0.191  -7.9351  -2.1028   0.3029
 M7T  H23  H  HCH2  0   0.233  -7.8481  -1.6978  -1.4155
 M7T  H24  H  HCH2  0   0.234  -7.4803  -4.2808  -0.4591
 M7T  H25  H  HCH2  0   0.235  -6.6684  -3.7235  -1.9115
 M7T  H26  H  HCH2  0   0.233  -5.3575  -4.3832   0.6189
 M7T  H27  H  HCH2  0   0.233  -4.6114  -3.7853  -0.8531
 M7T  H28  H  HCH2  0   0.234  -4.2132  -1.8740   0.5269
 M7T  H29  H  HCH2  0   0.191  -5.6253  -2.2158   1.5331

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 M7T  C8   C9   single    1.544  0.020  1.544
 M7T  C8   C7   single    1.529  0.020  1.529
 M7T  C9   C10  single    1.530  0.020  1.530
 M7T  C7   N1   single    1.452  0.020  1.452
 M7T  C10  N1   single    1.453  0.020  1.453
 M7T  N1   C6   single    1.442  0.020  1.442
 M7T  C6   C5   single    1.506  0.020  1.506
 M7T  C11  C5   aromatic  1.396  0.020  1.396
 M7T  C11  C12  aromatic  1.384  0.020  1.384
 M7T  C5   C4   aromatic  1.388  0.020  1.388
 M7T  C12  C2   aromatic  1.395  0.020  1.395
 M7T  C4   C3   aromatic  1.391  0.020  1.391
 M7T  C2   C1   single    1.505  0.020  1.505
 M7T  C2   C3   aromatic  1.388  0.020  1.388
 M7T  C1   N    single    1.448  0.020  1.448
 M7T  O    C    double    1.226  0.020  1.226
 M7T  N    C    single    1.360  0.020  1.360
 M7T  C    N2   single    1.373  0.020  1.373
 M7T  N2   C13  single    1.452  0.020  1.452
 M7T  N2   C20  single    1.451  0.020  1.451
 M7T  C13  C14  single    1.519  0.020  1.519
 M7T  C20  C21  single    1.523  0.020  1.523
 M7T  C14  N3   single    1.453  0.020  1.453
 M7T  C21  N3   single    1.453  0.020  1.453
 M7T  N3   C15  single    1.353  0.020  1.353
 M7T  C15  C16  single    1.485  0.020  1.485
 M7T  C15  O1   double    1.222  0.020  1.222
 M7T  C17  C16  aromatic  1.365  0.020  1.365
 M7T  C17  C18  aromatic  1.418  0.020  1.418
 M7T  C16  S    aromatic  1.724  0.020  1.724
 M7T  C18  C19  aromatic  1.363  0.020  1.363
 M7T  C19  S    aromatic  1.709  0.020  1.709
 M7T  C19  H1   single    0.930  0.020  1.080
 M7T  C18  H2   single    0.930  0.020  1.080
 M7T  C17  H3   single    0.930  0.020  1.080
 M7T  C14  H4   single    0.970  0.020  1.090
 M7T  C14  H5   single    0.970  0.020  1.090
 M7T  C13  H6   single    0.970  0.020  1.090
 M7T  C13  H7   single    0.970  0.020  1.090
 M7T  C21  H8   single    0.970  0.020  1.090
 M7T  C21  H9   single    0.970  0.020  1.090
 M7T  C20  H10  single    0.970  0.020  1.090
 M7T  C20  H11  single    0.970  0.020  1.090
 M7T  N    H12  single    0.890  0.020  1.040
 M7T  C1   H13  single    0.970  0.020  1.090
 M7T  C1   H14  single    0.970  0.020  1.090
 M7T  C12  H15  single    0.930  0.020  1.080
 M7T  C11  H16  single    0.930  0.020  1.080
 M7T  C4   H17  single    0.930  0.020  1.080
 M7T  C3   H18  single    0.930  0.020  1.080
 M7T  C6   H19  single    0.970  0.020  1.090
 M7T  C6   H20  single    0.970  0.020  1.090
 M7T  C10  H22  single    0.970  0.020  1.090
 M7T  C10  H23  single    0.970  0.020  1.090
 M7T  C9   H24  single    0.970  0.020  1.090
 M7T  C9   H25  single    0.970  0.020  1.090
 M7T  C8   H26  single    0.970  0.020  1.090
 M7T  C8   H27  single    0.970  0.020  1.090
 M7T  C7   H28  single    0.970  0.020  1.090
 M7T  C7   H29  single    0.970  0.020  1.090

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 M7T  N3   C15  C16  117.78  3.000
 M7T  C16  C15  O1   118.99  3.000
 M7T  N3   C15  O1   123.17  3.000
 M7T  C17  C16  S    110.96  3.000
 M7T  S    C16  C15  123.16  3.000
 M7T  C17  C16  C15  125.47  3.000
 M7T  C19  S    C16   91.95  3.000
 M7T  H1   C19  C18  128.09  3.000
 M7T  H1   C19  S    120.14  3.000
 M7T  C18  C19  S    111.77  3.000
 M7T  H2   C18  C17  124.02  3.000
 M7T  H2   C18  C19  123.51  3.000
 M7T  C17  C18  C19  112.47  3.000
 M7T  H3   C17  C18  124.00  3.000
 M7T  H3   C17  C16  123.16  3.000
 M7T  C18  C17  C16  112.84  3.000
 M7T  C21  N3   C14  112.18  3.000
 M7T  C21  N3   C15  125.01  3.000
 M7T  C14  N3   C15  120.18  3.000
 M7T  H5   C14  H4   107.97  3.000
 M7T  H5   C14  C13  109.94  3.000
 M7T  H4   C14  C13  109.29  3.000
 M7T  H5   C14  N3   110.00  3.000
 M7T  H4   C14  N3   107.94  3.000
 M7T  C13  C14  N3   111.61  3.000
 M7T  H7   C13  H6   107.68  3.000
 M7T  H7   C13  N2   110.72  3.000
 M7T  H6   C13  N2   109.82  3.000
 M7T  H7   C13  C14  109.86  3.000
 M7T  H6   C13  C14  108.89  3.000
 M7T  N2   C13  C14  109.83  3.000
 M7T  H9   C21  H8   107.95  3.000
 M7T  H9   C21  C20  109.96  3.000
 M7T  H8   C21  C20  108.05  3.000
 M7T  H9   C21  N3   109.33  3.000
 M7T  H8   C21  N3   111.06  3.000
 M7T  C20  C21  N3   110.45  3.000
 M7T  H11  C20  H10  106.98  3.000
 M7T  H11  C20  N2   112.09  3.000
 M7T  H10  C20  N2   110.06  3.000
 M7T  H11  C20  C21  107.43  3.000
 M7T  H10  C20  C21  109.07  3.000
 M7T  N2   C20  C21  111.06  3.000
 M7T  C    N2   C20  123.87  3.000
 M7T  C20  N2   C13  112.74  3.000
 M7T  C    N2   C13  118.35  3.000
 M7T  N    C    O    121.60  3.000
 M7T  N    C    N2   116.48  3.000
 M7T  O    C    N2   121.92  3.000
 M7T  H12  N    C1   115.41  3.000
 M7T  H12  N    C    119.21  3.000
 M7T  C1   N    C    120.95  3.000
 M7T  H14  C1   H13  106.85  3.000
 M7T  H14  C1   C2   109.75  3.000
 M7T  H13  C1   C2   109.73  3.000
 M7T  H14  C1   N    108.53  3.000
 M7T  H13  C1   N    111.81  3.000
 M7T  C2   C1   N    110.10  3.000
 M7T  C3   C2   C12  118.39  3.000
 M7T  C3   C2   C1   121.13  3.000
 M7T  C12  C2   C1   120.48  3.000
 M7T  H15  C12  C11  119.53  3.000
 M7T  H15  C12  C2   119.64  3.000
 M7T  C11  C12  C2   120.84  3.000
 M7T  H16  C11  C5   119.20  3.000
 M7T  H16  C11  C12  120.01  3.000
 M7T  C5   C11  C12  120.79  3.000
 M7T  C6   C5   C4   120.87  3.000
 M7T  C4   C5   C11  118.34  3.000
 M7T  C6   C5   C11  120.78  3.000
 M7T  H17  C4   C3   119.40  3.000
 M7T  H17  C4   C5   119.70  3.000
 M7T  C3   C4   C5   120.89  3.000
 M7T  H18  C3   C4   119.55  3.000
 M7T  H18  C3   C2   119.70  3.000
 M7T  C4   C3   C2   120.75  3.000
 M7T  H20  C6   H19  106.05  3.000
 M7T  H20  C6   N1   108.01  3.000
 M7T  H19  C6   N1   111.77  3.000
 M7T  H20  C6   C5   108.82  3.000
 M7T  H19  C6   C5   109.22  3.000
 M7T  N1   C6   C5   112.70  3.000
 M7T  C7   N1   C10  104.66  3.000
 M7T  C10  N1   C6   113.49  3.000
 M7T  C7   N1   C6   114.38  3.000
 M7T  H23  C10  H22  107.27  3.000
 M7T  H23  C10  C9   113.46  3.000
 M7T  H22  C10  C9   110.06  3.000
 M7T  H23  C10  N1   110.87  3.000
 M7T  H22  C10  N1   111.40  3.000
 M7T  C9   C10  N1   103.85  3.000
 M7T  H25  C9   H24  107.23  3.000
 M7T  H25  C9   C8   110.72  3.000
 M7T  H24  C9   C8   112.59  3.000
 M7T  H25  C9   C10  110.86  3.000
 M7T  H24  C9   C10  111.25  3.000
 M7T  C8   C9   C10  104.25  3.000
 M7T  H27  C8   H26  107.27  3.000
 M7T  H27  C8   C7   110.61  3.000
 M7T  H26  C8   C7   111.40  3.000
 M7T  H27  C8   C9   110.62  3.000
 M7T  H26  C8   C9   112.67  3.000
 M7T  C7   C8   C9   104.32  3.000
 M7T  H29  C7   H28  107.26  3.000
 M7T  H29  C7   C8   110.39  3.000
 M7T  H28  C7   C8   113.03  3.000
 M7T  H29  C7   N1   111.20  3.000
 M7T  H28  C7   N1   111.45  3.000
 M7T  C8   C7   N1   103.57  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 M7T  CONST_01  C19  C18  C17  C16    0.00   0.0  0
 M7T  CONST_02  C18  C19  S    C16    0.00   0.0  0
 M7T  CONST_03  C18  C17  C16  S      0.00   0.0  0
 M7T  CONST_04  C17  C18  C19  S      0.00   0.0  0
 M7T  CONST_05  C17  C16  S    C19    0.00   0.0  0
 M7T  CONST_06  C5   C11  C12  C2     0.00   0.0  0
 M7T  CONST_07  C5   C4   C3   C2     0.00   0.0  0
 M7T  CONST_08  C4   C5   C11  C12    0.00   0.0  0
 M7T  CONST_09  C4   C3   C2   C12    0.00   0.0  0
 M7T  CONST_10  C3   C4   C5   C11    0.00   0.0  0
 M7T  CONST_11  C3   C2   C12  C11    0.00   0.0  0
 M7T  CONST_12  C18  C17  C16  C15  180.00   0.0  0
 M7T  CONST_13  C19  S    C16  C15  180.00   0.0  0
 M7T  CONST_14  C11  C12  C2   C1   180.00   0.0  0
 M7T  CONST_15  C4   C3   C2   C1   180.00   0.0  0
 M7T  CONST_16  C6   C5   C11  C12  180.00   0.0  0
 M7T  CONST_17  C6   C5   C4   C3   180.00   0.0  0
 M7T  CONST_18  C14  N3   C15  C16  180.00   0.0  0
 M7T  CONST_20  H2   C18  C17  C16  180.00   0.0  0
 M7T  CONST_21  H1   C19  S    C16  180.00   0.0  0
 M7T  CONST_22  H3   C17  C16  S    180.00   0.0  0
 M7T  CONST_23  H16  C11  C12  C2   180.00   0.0  0
 M7T  CONST_24  H17  C4   C3   C2   180.00   0.0  0
 M7T  CONST_25  H18  C3   C2   C12  180.00   0.0  0
 M7T  CONST_26  H15  C12  C11  C5   180.00   0.0  0
 M7T  CONST_27  C14  N3   C15  O1     0.00   0.0  0
 M7T  CONST_29  O    C    N2   C13    0.00   0.0  0
 M7T  CONST_31  N    C    N2   C13  180.00   0.0  0
 M7T  CONST_33  C1   N    C    N2   180.00   0.0  0
 M7T  CONST_35  C1   N    C    O      0.00   0.0  0
 M7T  Var_01    N2   C13  C14  N3    54.77  30.0  1
 M7T  Var_02    N2   C20  C21  N3   -54.31  30.0  1
 M7T  Var_03    C20  N2   C13  C14  -55.44  30.0  1
 M7T  Var_04    C20  C21  N3   C14   54.93  30.0  1
 M7T  Var_05    C21  C20  N2   C13   55.85  30.0  1
 M7T  Var_06    C21  N3   C14  C13  -55.84  30.0  1
 M7T  Var_07    C9   C8   C7   N1   -26.33  30.0  1
 M7T  Var_08    C8   C9   C10  N1    24.59  30.0  1
 M7T  Var_09    C7   C8   C9   C10    1.05  30.0  1
 M7T  Var_10    C8   C7   N1   C10   43.30  30.0  1
 M7T  Var_11    C7   N1   C10  C9   -42.66  30.0  1
 M7T  Var_12    N3   C15  C16  S    -47.24  30.0  2
 M7T  Var_13    N1   C6   C5   C11   42.35  30.0  1
 M7T  Var_14    C12  C2   C1   N    -61.32  30.0  2
 M7T  Var_15    C2   C1   N    C    162.74  30.0  1

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 M7T  plan-1  C15  0.020
 M7T  plan-1  C16  0.020
 M7T  plan-1  S    0.020
 M7T  plan-1  C19  0.020
 M7T  plan-1  C18  0.020
 M7T  plan-1  C17  0.020
 M7T  plan-1  H1   0.020
 M7T  plan-1  H2   0.020
 M7T  plan-1  H3   0.020
 M7T  plan-2  O1   0.020
 M7T  plan-2  C15  0.020
 M7T  plan-2  C16  0.020
 M7T  plan-2  N3   0.020
 M7T  plan-2  C14  0.020
 M7T  plan-2  C21  0.020
 M7T  plan-3  C1   0.020
 M7T  plan-3  C2   0.020
 M7T  plan-3  C12  0.020
 M7T  plan-3  C11  0.020
 M7T  plan-3  C5   0.020
 M7T  plan-3  C4   0.020
 M7T  plan-3  C3   0.020
 M7T  plan-3  C6   0.020
 M7T  plan-3  H15  0.020
 M7T  plan-3  H16  0.020
 M7T  plan-3  H17  0.020
 M7T  plan-3  H18  0.020
 M7T  plan-4  C13  0.020
 M7T  plan-4  C20  0.020
 M7T  plan-4  N2   0.020
 M7T  plan-4  C    0.020
 M7T  plan-4  O    0.020
 M7T  plan-4  N    0.020
 M7T  plan-4  C1   0.020
 M7T  plan-4  H12  0.020

